diff --git a/rosetta_basics/Rosetta-Basics.md b/rosetta_basics/Rosetta-Basics.md index 9252c6027..db1255b22 100644 --- a/rosetta_basics/Rosetta-Basics.md +++ b/rosetta_basics/Rosetta-Basics.md @@ -45,6 +45,7 @@ * [[Design-centric guidance terms|design-guidance-terms]] * [[Hydrogen bonding score term|hbonds]] * [[Centroid score terms]] + * [[Quantum mechanical energy calculations in Rosetta | qm-energy-calculations ]] - [[Symmetry]] - [[Minimization | Minimization Overview]] - Backbone and/or side chain degrees of freedom - [[Comparing Structures]] diff --git a/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSPointEnergyTutorial1.md b/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSPointEnergyTutorial1.md new file mode 100644 index 000000000..36ef9322f --- /dev/null +++ b/rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSPointEnergyTutorial1.md @@ -0,0 +1,34 @@ +# GAMESS Point Energy Tutorial 1: Running SPE calculation on a cyclic peptide of known structure + +[[Back to Quantum mechanical energy calculations in Rosetta|qm-energy-calculations]] + +## GAMESS Point Energy Tutorial 1: Running SPE calculation on a cyclic peptide of known structure + +A single point energy (SPE) calculation with GAMESS can be run through Rosetta directly from the command line. Depending on the user preference, user can either use an XML script or run directly from the command-line interface. Here we will quickly go through two tutorials to demonstrate how this can be done. + + +Say we want to know what is the SPE of the peptide 5vav (PDB ID). To do this we first download the structure from PDB. Next we need to create a file which will serve as the flags file for both Rosetta (and GAMESS through Rosetta). We are going to call this file rosetta.flags. Within this flags file we will give the following options: + +----------------------------------------------------------------------------------- +-in:file:s 5vav.pdb +-in:file:fullatom true +-score:weights gamess_qm.wts +-GAMESS_executable_version 00 +-GAMESS_path /home/bturzo/gamess +-quantum_mechanics::GAMESS::rosetta_GAMESS_bridge_temp_directory ./ +-quantum_mechanics::GAMESS::clean_rosetta_GAMESS_bridge_temp_directory false +-quantum_mechanics::GAMESS::clean_GAMESS_scratch_directory false +-quantum_mechanics::GAMESS::GAMESS_threads 10 +-quantum_mechanics:GAMESS:gamess_qm_energy_geo_opt false +-out:levels core.quantum_mechanics.RosettaQMDiskAccessManager_GAMESS_Output:500 +----------------------------------------------------------------------------------- + +In this example, +-in:file:s is used to indicate the pdb (5vav.pdb) on which we are going to run our SPE calculation. +-in:file:fullatom is used to enable full-atom input of PDB (Vikram is this option required?). +-score:weights flag enables the QM score term if the weights file (gamess_qm.wts) consists the line. Additionally the weights file can be used to add further options for GAMESS (discussed later). +-quantum_mechanics::GAMESS::rosetta_GAMESS_bridge_temp_directory flag creates three files .err, .inp, and .log. In this example it will create these three files in the current directory. The .inp file consists of the input that was created for GAMESS. The .log and .err files contain the output and error (respectively) from GAMESS during the runtime. + +--------------------- +gamess_qm_energy 1.0 +--------------------- diff --git a/rosetta_basics/scoring/qm-energy-calculations.md b/rosetta_basics/scoring/qm-energy-calculations.md new file mode 100644 index 000000000..1ef1b2c05 --- /dev/null +++ b/rosetta_basics/scoring/qm-energy-calculations.md @@ -0,0 +1,99 @@ +# Quantum mechanical energy calculations in Rosetta + +Back to [[Rosetta basics|Rosetta-Basics]]. +Page created 16 November 2021 by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org). + +[[_TOC_]] + +## Summary + +Traditionally, Rosetta has used a quasi-Newtonian force field for energy calculations. This has allowed Rosetta protocols to score a large macromolecular structure rapidly (typically in milliseconds) and repeatedly, permitting large-scale sampling of conformation and/or sequence space. The downside, however, has been that force fields are of finite accuracy. In late 2021, we added support for carrying out quantum mechanical energy and geometry optimization calculations in the context of a Rosetta protocol, by calling out to a third-party quantum chemistry software package. This page summarizes how to set up and use this functionality. + +## Important considerations + +### Molecular system size, level of theory, and computation time + +TODO + +### Computer memory + +TODO + +### CPU usage (especially in multi-threaded or multi-process contexts) + +TODO + +### Disk usage + +TODO + +## Supported third-party quantum chemistry software packages + +All Rosetta QM calculations are performed through calls to third-party quantum chemistry software packages. These must be downloaded and installed separately, and users must have appropriate licences and privilegse to use these. Supported packages include: + +### The General Atomic and Molecular Electronic Structure System (GAMESS) + +[[GAMESS|https://www.msg.chem.iastate.edu/index.html]] is a versatile quantum chemistry package written in FORTRAN, and developed by the [[Gordon group at Iowa State University|https://www.msg.chem.iastate.edu/group/members.html]]. Users may agree to the licence agreement and obtain the software from [[the GAMESS download page|https://www.msg.chem.iastate.edu/gamess/download.html]]. + +#### Installation and setup + +To use GAMESS with Rosetta... TODO + +#### Compiling GAMESS + +#### Using GAMESS with Rosetta + +##### Point energy calculations with GAMESS within a Rosetta protocol + +A single point energy (SPE) calculation with GAMESS can be run through Rosetta directly from the command line. Depending on the user preference, the user can either use an XML script or run directly from the command-line interface. Here are two tutorials to demonstrate how this can be done: + +[[Tutorial #1|GAMESSPointEnergyTutorial1]] +[[Tutorial #2|GAMESSPointEnergyTutorial2]] + +###### Dealing with the influence of solvent + +When modelling biological macromolecules, the effect of solvent cannot be discounted. Indeed, the hydrohobic effect is the dominant effect that causes proteins to fold. Solvent affects computed energies in two ways. First, there is the enthalpy of interaction of a biomolecule with the surrounding solvent. Second, the shape and interacting groups presented by a molecule infuence solvent entropy. The hydrohobic effect is largely an entropic effect: hydrophobic groups that are unable to form hydrogen bonds with water force an ordering of water molecules when they are solvated, since the accessible low-enthalpy states, in which water molecules satisfy their hydrogen bonds by bonding to one another, are fewer when some water conformations are effectively prohibited by the presence of a non-hydrogen bonding group. + +GAMESS can model solvent effects in three ways: + +1. By ignoring them completely. This is equivalent to modelling the macromolecule in vacuum, and can be achieved by setting `-quantum_mechanics:GAMESS:default_solvent GAS` on the commandline, or `gamess_solvent="GAS"` in the scoring function setup. In most circumstances, this is not advised: one would not expect a protein to fold, for instance, if water is not present. + +2. By modelling only electrostatic interactions with the solvent, and electrostatic screening effects. The default PCM (polarizable continuum) model, with solvent set to the default value of `WATER`, will do this. This is roughly equivalent to explicitly modelling water molecules and carrying out a vacuum calculation, up to the limits of accuracy of any continuum (implicit solvent) model. This does _not_ capture the effects of the macromolecule's conformation on solvent entropy. Again, this is not advised in most circumstances. However, since the `gamess_qm_energy` is a scoring _term_ and not an independent scoring _function_, one can use a sum of QM and molecular mechanics terms to capture solvent enthalpy and entropy. For instance: + +```xml + + + + + + + + + +``` + +3. By modelling electrostatic interactions with the water, plus _c_avitation, _d_ispersion, and local solvent _s_tructure effects (CSD model) using an empirically-fitted SMD (solvation model density) model. The CSD part of the SMD model approximates the entropic effects, though this has not been widely tested for biological macromolecules, particuarly to simulate solvent entropy-mediated effects like protein folding. In theory, this model should be more general than Rosetta's solvation model, though, and should support a wider range of solvents (including many organic solvents). To enable the SMD solvation model, set `quantum_mechanics:GAMESS:default_use_smd_solvent true` on the commandline, or `gamess_use_smd_solvent="true"` in the scorefunction settings. + +##### Geometry optimization with GAMESS within a Rosetta protocol + +TODO + +##### Transition state identification with GAMESS within a Rosetta protocol + +TODO + +#### Rosetta-GAMESS bridge code organization + +TODO + +### Psi4 + +TODO + +### Orca + +TODO + +### NWChem + +TODO diff --git a/scripting_documentation/RosettaScripts/RosettaScripts.md b/scripting_documentation/RosettaScripts/RosettaScripts.md index 8162b50ea..1d3c24c81 100644 --- a/scripting_documentation/RosettaScripts/RosettaScripts.md +++ b/scripting_documentation/RosettaScripts/RosettaScripts.md @@ -248,7 +248,7 @@ apps.public.rosetta_scripts.rosetta_scripts: apps.public.rosetta_scripts.rosetta_scripts: The rosetta_scripts application will now exit. ``` -You can also get help on the syntax of any mover, filter, task operation, or residue selector using the `-parser:info ...` flag. For example, the following commandline will provide information on the [[MutateResidue|MutateResidueMover]] mover and the [[HbondsToAtom|HbondsToAtomFilter]] filter: +You can also get help on the syntax of any mover, filter, task operation, packer palette, scorefunction, or residue selector using the `-parser:info ...` flag. For example, the following commandline will provide information on the [[MutateResidue|MutateResidueMover]] mover and the [[HbondsToAtom|HbondsToAtomFilter]] filter: ``` ./bin/rosetta_scripts.default.linuxgccrelease -info MutateResidue HbondsToAtom @@ -910,4 +910,4 @@ Another good troubleshooting tool is to simplify your XML. Try creating a stripp \ No newline at end of file +--> diff --git a/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md b/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md index 48897f8c8..610fb8ad8 100644 --- a/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md +++ b/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md @@ -34,7 +34,7 @@ The trRosettaConstraintGenerator requires compilation with Tensorflow support. References and author information for the trRosettaConstraintGenerator constraint generator: -trRosetta Neural Network's citation(s): +trRosetta neural network's citation(s): Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, and Baker D. (2020). Improved protein structure prediction using predicted interresidue orientations. Proc Natl Acad Sci USA 117(3):1496-503. doi: 10.1073/pnas.1914677117. trRosettaConstraintGenerator ConstraintGenerator's author(s): diff --git a/scripting_documentation/RosettaScripts/xsd/filter_Ddg_type.md b/scripting_documentation/RosettaScripts/xsd/filter_Ddg_type.md index e0a11b4d8..5f6c7bbc7 100644 --- a/scripting_documentation/RosettaScripts/xsd/filter_Ddg_type.md +++ b/scripting_documentation/RosettaScripts/xsd/filter_Ddg_type.md @@ -14,9 +14,10 @@ Computes the binding energy for the complex and if it is below the threshold ret relax_unbound="(true &bool;)" translate_by="(100 ℜ)" relax_mover="(&string;)" filter="(&string;)" chain_num="(&string;)" extreme_value_removal="(false &bool;)" dump_pdbs="(false &bool;)" + enable_caching="(false &bool;)" task_operations="(&task_operation_comma_separated_list;)" packer_palette="(&named_packer_palette;)" scorefxn="(&string;)" - confidence="(1.0 ℜ)" /> + final_scorefxn="(&string;)" confidence="(1.0 ℜ)" /> ``` - **threshold**: If ddG value is lower than this value, filter returns True (passes). @@ -36,9 +37,11 @@ Computes the binding energy for the complex and if it is below the threshold ret - **chain_num**: Allows you to specify a list of chain numbers to use to calculate the ddg, rather than a single jump. You cannot move chain 1, moving all the other chains is the same thing as moving chain 1, so do that instead. Use independently of jump. - **extreme_value_removal**: Compute ddg value times, sort and remove the top and bottom evaluation. This should reduce the noise levels in trajectories involving 1000s of evaluations. If set to true, repeats must be set to at least 3. - **dump_pdbs**: Dump debugging PDB files. Dumps 6 pdbs per instance: BOUND_before_repack, BOUND_after_repack, BOUND_after_relax, UNBOUND_before_repack, UNBOUND_after_repack, and UNBOUND_after_relax. +- **enable_caching**: Cache DDG calculations to avoid re-computing during reporting. Each time this object is called it will reset the cache when compute() is run, so it can be used on unique poses. Please note that caching requires updating a data member, which means that if this object is shared by multiple threads there will be data racing (i.e., not thread-safe). - **task_operations**: A comma-separated list of TaskOperations to use. - **packer_palette**: A previously-defined PackerPalette to use, which specifies the set of residue types with which to design (to be pruned with TaskOperations). - **scorefxn**: Name of score function to use +- **final_scorefxn**: A scoring function to use for final scoring of the docked and undocked poses (to compute the difference). If not provided, the scoring function provided with the scorefxn option is used. The option of scoring with a different final scoring function is provided to allow a more accurate, more expensive calculation to be done for this (e.g. using RosettaQM quantum chemistry calculations). - **confidence**: Probability that the pose will be filtered out if it does not pass this Filter --- diff --git a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md b/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md index 4c98b1ff6..73c5d1980 100644 --- a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md +++ b/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md @@ -13,7 +13,7 @@ Filter based on any score that can be calculated in fragment_picker. outputs_name="(pose &string;)" csblast="(&string;)" blast_pgp="(&string;)" placeholder_seqs="(&string;)" sparks-x="(&string;)" sparks-x_query="(&string;)" psipred="(&string;)" - vall_path="(/home/benchmark/rosetta/database//sampling/vall.jul19.2011.gz &string;)" + vall_path="(/Users/vmulligan/rosetta_devcopy/Rosetta/main/database//sampling/vall.jul19.2011.gz &string;)" frags_scoring_config="(&string;)" n_frags="(200 &non_negative_integer;)" n_candidates="(1000 &non_negative_integer;)" print_to_pdb="(false &xs:boolean;)" diff --git a/scripting_documentation/RosettaScripts/xsd/mover_GamessQMGeometryOptimizationMover_type.md b/scripting_documentation/RosettaScripts/xsd/mover_GamessQMGeometryOptimizationMover_type.md new file mode 100644 index 000000000..8e1178da7 --- /dev/null +++ b/scripting_documentation/RosettaScripts/xsd/mover_GamessQMGeometryOptimizationMover_type.md @@ -0,0 +1,123 @@ + + +_Autogenerated Tag Syntax Documentation:_ + +--- +A mover that relaxes a Pose based on a GAMESS QM geometry optimization calculation. This mover calls out to the GAMESS software package, which carries out gradient-descent optimization of nuclear positions (in Cartesian space) to minimize quantum mechanical energy. + +References and author information for the GamessQMGeometryOptimizationMover mover: + +GamessQMGeometryOptimizationMover Mover's author(s): +Benjamin P. Brown, Department of Chemistry, Vanderbilt University [benjamin.p.brown17@gmail.com] (Wrote the GamessQMGeometryOptimizationMover) +Vikram K. Mulligan, Systems Biology Group, Center for Computational Biology, Flatiron Institute [vmulligan@flatironinstitute.org] (Contributed to GamessQMGeometryOptimizationMover (symmetry support, etc.).) + +```xml + +``` + +- **gamess_path**: Path to GAMESS rungms executable (not including executable name). If not specified, defaults to path set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_path option. +- **gamess_executable_version**: GAMESS executable version. Typically, this is a two-digit string, like 00 or 01. If not specified, this defaults to the executable version specified on the commandline with the -quantum_mechanics:GAMESS:GAMESS_executable_version option. +- **gamess_memory_megabytes**: The amount of memory, in megabytes, that each GAMESS process is allowed to use. Defaults to 8,192 megabytes, or whatever is set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_memory_megabytes commandline flag. +- **gamess_threads**: The number of GAMESS threads to launch. Use 0 to launch one GAMESS thread per hardware thread on the node. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_threads commandline flag. +- **gamess_processes_per_node**: The number of GAMESS MPI processes to launch per node per calling Rosetta thread or process. Use 0 to launch one GAMESS MPI process per hardware thread on the node. Only used if MPI build of GAMESS is used. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_processes_per_node commandline flag. +- **use_gamess_mpi**: If true, the MPI build of GAMESS will be used (which requires a value for gamess processes per node). If not specified, defaults to the commandline setting, based on whether the -quantum_mechanics:GAMESS:GAMESS_processes_per_node option is provided. +- **rosetta_gamess_bridge_temp_directory**: The location of the directory to which we will write temporary files to allow Rosetta to communicate with GAMESS. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:rosetta_GAMESS_bridge_temp_directory commandline flag. +- **clean_rosetta_gamess_bridge_temp_directory**: If true, temporary files written during the Rosetta-GAMESS bridge scratch directory will be deleted. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:clean_rosetta_GAMESS_bridge_temp_directory commandline flag. +- **clean_gamess_scratch_directory**: If true, GAMESS temporary files written during the calculation will be deleted. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:clean_GAMESS_scratch_directory commandline flag. +- **gamess_qm_energy_file_prefix**: The prefix to use for temporary files written by the gamess_qm_energy energy method. Generally, one needn't change this, but it can be useful if one has many instances of Rosetta running on the same system and using the same GAMESS scratch directory or GAMESS supplemental output directory. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_qm_energy_file_prefix commandline flag. +- **gamess_hybrid_molecular_orbital_file**: The path and filename of the GAMESS HMOs.txt file. This is only used for fragment molecular orbital (FMO) calculations. This can be a relative path from the directory that contains the rungms executable or an absolute path. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_hybrid_molecular_orbital_file commandline flag (and rarely needs to be changed). +- **gamess_verbosity**: The overall verbosity level for the GAMESS output log. Allowed options are 'maximal', 'normal', and 'minimal', and these correspond to NPRINT=9, NPRINT=7, and NPRINT=-5, respectively, in the $CONTRL block of the GAMESS input file. Note that fragment molecular orbital (FMO) verbosity is set separately with the default_fmo_verbosity flag. If not specified, this defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:default_verbosity commandline flag. +- **solvent**: The solvent to use. Common choics are GAS (no solvent) and WATER. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_solvent flag. +- **use_smd_solvent**: If true, use the Solvation Model Density (SMD) with CDS corrections; otherwise, use a standard polarizable continuum model for solvation. +- **basis_set**: The basis set to use for point energy calculation. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_basis_set flag. +- **ngaussian**: The number of Gaussians to include in the basis set. Only used for some basis sets. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_ngaussian flag. +- **npfunc**: The number of light-atom (H, He) P-orbital basis functions to include in the basis set. Not used by all basis functions; see the GAMESS documentation for details. Maximum 3. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_npfunc flag. +- **ndfunc**: The number of heavyatom D-orbital basis functions to include in the basis set. Not used by all basis functions; see the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_ndfunc flag. +- **nffunc**: The number of heavyatom F-orbital basis functions to include in the basis set. Not used by all basis functions; see the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_nffunc flag. +- **diffsp**: Should a diffuse SP shell be added to heavyatoms? See the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_diffsp flag. +- **diffs**: Should a diffuse S shell be added to hydrogen atoms? See the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_diffs flag. +- **dft_functional**: The DFT functional to use, if density functional theory is specified. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_dft_functional flag. +- **dft_dispersion_corrections**: The DFT dispersion correction to use, specified as an integer. Use -1 to use GAMESS default, 0 for None, 1 for Grimme's DC 2004, 2 for Grimme's DC 2006 (DFT-D2, the default in wB97X-D and B97-D), 3 for Grimme's DC 2010 (DFT-D3, GAMESS default if DC is requested), or 4 for modified DFT-D3 (DFT-D3(BJ), the default for HF-3C). If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_dft_dispersion_corrections flag. +- **multiplicity**: The multiplicity. Typically 1, unless free radicals are present. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_multiplicity flag. +- **electron_correlation_treatment**: The electron correlation treatment. Options are HF, SE (semi-empirical), MP2 (Moller-Plesset perturbation theory 2nd order corrections), or DFT (density functional theory). If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_electron_correlation_treatment flag. +- **max_scf_iterations**: The number of self-consistent field iteration cycles. A setting of 0 (the default) uses the GAMESS default (which is 30 in most circumstances). It is recommended to set this higher for larger peptides or for any protein. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_max_scf_iterations flag. +- **use_scf_damping**: If true, Davidson damping is applied to aid SCF convergence when doing GAMESS calculations. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:default_use_scf_damping flag. +- **fmo_calculation**: If true, we perform a fragment molecular orbital calculation based on the rules set in the scorefunction for dividing a pose into fragments. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_fmo_calculation flag. +- **max_fmo_monomer_scf_iterations**: The maximum number of monomer SCF iterations to perform by default. If not provided, defaults to whatever is provided on the commandline with the -quantum_mechanics:GAMESS:default_max_fmo_monomer_scf_iterations flag. +- **hybrid_molecular_orbital**: The precomputed hybrid molecular orbital, listed in the GAMESS HMOs.txt file, that should be used at cutpoint atoms when doing a fragment molecular orbital calculation with GAMESS. Only used for FMO calculations. If not specified, defaults to whatever is specified on the commandline with the -quantum_mechanics:GAMESS:gamess_hybrid_molecular_orbital flag. +- **symmetry**: The symmetry expected by the gamess_qm_energy energy term. NONE can always be used, though for symmetric molecules, this makes the QM calculation less efficient than it could be. Allowed types are: NONE, Cn, Dn, and Sn. The symmetry of the pose must match the symmetry specfied! If not specified, this defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_qm_energy_symmetry flag. +- **symmetry_n**: The n-fold symmetry expected by the gamess_qm_energy energy term. This must be an integer greater than 1 if symmetry is Cn or Dn, and an even integer greater than 1 if symmetry is Sn. Not used if symmetry is NONE. +- **fmo_verbosity**: The amount of output in the logfile from an FMO calculation. The options 'normal', 'reduced', 'small', and 'minimal' correspond to NPRINT=0, 1, 2, and 3 respectively in the $FMOPRP group in the GAMESS input file. If not specified, defaults to whatever is specified on the commandline with the -quantum_mechanics:GAMESS:fmo_verbosity option. +- **error_on_nonideal_bond_length_after_opt**: If true, Rosetta will throw an error if a GAMESS geometry optimization breaks a covalent bond (results in nonideal bond lengths over or under a threshold). If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_error_on_nonideal_bond_length_after_opt flag. +- **nonideal_bond_length_fract_threshold**: The fractional threshold for detecting nonideal bond lenghts. For example, if set to 0.35, Rosetta throws an error if any bond is detected that is 35% longer or shorter than ideal after GAMESS geometry optimization. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_nonideal_bond_length_fract_threshold flag. +- **geo_opt_max_steps**: The maximum number of geometry optimization steps that will be carried out, if GAMESS is optimizing geometry. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_max_steps flag. +- **geo_opt_tolerance**: The tolerance for geometry optimization, if GAMESS is optimizing geometry. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_max_steps flag. +- **immobilize_h_bond_lengths**: If true, use GAMESS IFZMAT to freeze covalent bond lengths to hydrogen atoms to equilibrium values. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_immobilize_h_bond_lengths. +- **use_h_bond_length_constraints**: If true, use GAMESS IHMCON to harmonically constrain covalent bond lengths to hydrogen atoms to equilibrium values. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_constrain_h_bond_lengths. +- **h_bond_length_constraint_force**: If 'gamess_constrain_h_bond_lengths' is true and this flag is set, set the GAMESS FHMCON constraint force (kcal/mol) to this value. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_h_bond_length_constraint_force. +- **freeze_atoms_cart**: List of atom indices to be frozen during geometry optimization; set the GAMESS IFREEZ option to freeze an atom in Cartesian space; incompatible with NZVAR greater than 0 because the constraint is in Cartesian space; default behavior is to not freeze any atoms +- **freeze_atoms_by_res_cart**: Atoms given in the format 'ResNum.AtomName' to be frozen during geometry optimization; set the GAMESS IFREEZ option to freeze an atom in Cartesian space; incompatible with NZVAR greater than 0 because the constraint is in Cartesian space; default behavior is to not freeze any atoms +- **dftb_taylor_expansion_order**: The density functional tight binding (DFTB) semi-empirical method is fast since it uses only the first few terms of a Taylor series expansion of the Kohn/Sham DFT total energy. This parameter (equivalent to NDFTB in a GAMESS input file) determines how many terms to use. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_taylor_expansion_order; can be set to 1, 2, or 3. +- **use_dftb_long_range_correction**: This turns on the long range corretion to the DFTB semi-empirical method. Note that this requires parameters optimized for the long-range correction. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_use_dftb_long_range_correction. This is equivalent to the LCDFTB option in a GAMESS input file. +- **dftb_long_range_correction_parameter**: A configuration parameter for the DFTB long-range correction. Only used if use_dftb_long_range_correction is set to true. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_long_range_correction_parameter. See the EMU option in the GAMESS documentation for details. +- **use_dftb_damping_function_for_X_H**: If true, a damping function for X-H atomic pair interactions is included in the DFTB semi-empirical method. Requires dftb_taylor_expansion_order to be set to 3. See the DAMPXH option in the GAMESS documentation for details. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_use_dftb_damping_function_for_X_H. +- **dftb_damping_exponent_for_X_H**: The exponent for the damping function added for X-H atomic pairs. Only used if use_dftb_damping_function_for_X_H is set to true. If not provided, whatever is provided on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_damping_exponent_for_X_H is used. See the DAMPEX option in the GAMESS documentation for details. +- **use_dftb_shell_resolved_scc**: If true, shell-resolved SCC calculations are performed. Requires dftb_taylor_expansion_order to be set to 1 or 2. Defaults to whatever is provided on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_use_dftb_shell_resolved_scc. See the SRSCC option in the GAMESS documentation for details. +- **dftb_convergence_method**: The convergence method used for SCC calculations. Defaults to whatever is set on the commandline with the -quantum_mehanics:GAMESS:dftb:gamess_dftb_convergence_method option. Allowed values are standard, Broyden, DIIS. See the ITYPMX option in the GAMESS documentation for details. +- **dftb_electronic_temperature**: Electronic temperature in Kelvin to help convergence of nearly-degenerate systems. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_electronic_temperature. See the ETEMP option in the GAMESS documentation for details. +- **dftb_dispersion_model**: The dispersion correction model for DFTB calculations. Allowed values are NONE, UFF, SK, SKHP, and DFT. Defaults to whatever is set on the commandline with the -quantum_mehanics:GAMESS:dftb:gamess_dftb_dispersion_model option. See the DISP option in the GAMESS documentation for details. +- **dftb_parameters_directory**: The directory (relative to the GAMESS_path/auxdata/DFTB/ directory) in which DFTB parameters are found. If not set, the commandline option -quantum_mehanics:GAMESS:dftb:gamess_dftb_parameters_directory is used. If nothing is set here or on the commandline, this defaults to 3OB-3-1, which is suitable for Taylor expanson level 3 and aqueous solvent. See the PARAM option in the GAMESS documentation for details. +- **msfxn_name**: (optional) The name of the MultiScoreFunction to be used during geometry optimization; if not provided, then geometry optimization is performed over the entire pose using the quantum mechanical treatment set in this mover's other options; overrides QM options set in this mover. +- **msfxn_handler_type**: (optional) Geometry optimization with multiple levels of theory requires special handling of each sub-pose during and cutpoint during optimization. This option specifies the handler used for this task. +- **msfxn_classical_cartmin**: (optional) Perform Cartesian minimization on non-QM regions defined in the multiple score function. If true but the specified non-QM energy function does not contain Cartesian score terms, then it will automatically switch to false. +- **msfxn_freeze_cutpoint_atoms**: (optional) Freeze the coordinates of atoms connecting the current MultiScoreFunction region to any other region during geometry optimization / minimization +- **msfxn_freeze_noncommon_atoms**: (optional) Freeze the coordinates of atoms that are present in the the current MultiScoreFunction region but not common with atoms in the original pose (e.g., added capping groups or link atoms) during geometry optimization / minimization + +--- diff --git a/scripting_documentation/RosettaScripts/xsd/mover_GamessQMRunScanPoseMover_type.md b/scripting_documentation/RosettaScripts/xsd/mover_GamessQMRunScanPoseMover_type.md new file mode 100644 index 000000000..a0d71aab8 --- /dev/null +++ b/scripting_documentation/RosettaScripts/xsd/mover_GamessQMRunScanPoseMover_type.md @@ -0,0 +1,63 @@ + + +_Autogenerated Tag Syntax Documentation:_ + +--- +A quantum chemistry mover that increments atoms along a user-specified reaction coordinate and either (1) computes a single point energy calculation, or (2) performs a partial geometry optimization with reaction coordinate atoms fixed in Cartesian space, using the GAMESS quantum chemistry software package for the energy calculations and optimization. A scan that performs only single point energy calculations is referred to as a 'rigid scan', while a scan that performs a partial geometry optimization at each interval is referred to as a 'flexible scan'. If multiple scan points are provided, then the output structure will be selected based on several options: start, end, transition, lowest energy, or highest energy. Energies from each point of the scan will be output as individual score terms. + +References and author information for the GamessQMRunScanPoseMover mover: + +GamessQMRunScanPoseMover Mover's author(s): +Benjamin P. Brown, Research Assistant Professor, Department of Chemistry, Vanderbilt University [benjamin.p.brown17@gmail.com] (Wrote the GamessQMRunScanPoseMover.) + +```xml + + + + + +``` + +- **scan_type**: "rigid" (default) - compute single point energy at each scan interval; "flexible" - perform geometry optimization at each fixed scan interval +- **mover_name**: The QM geometry optimization mover whose execution is desired +- **metric_name**: The QM energy metric whose execution is desired +- **init_rc_from_original_coords**: If true then reset the pose coordinates to their original values before each reaction coordinate scan step; this causes subsequent geometry optimization to begin from the coordinates of the original pose, plus whatever perturbation is encoded in the reaction coordinate; if pose is not reset (i.e., 'false'), then each geometry optimization is initialized from the post-optimization coordinates of the last round, with the reaction coordinate scan applied in that context. +- **dump_pdb_rc_pre_opt**: Dump the PDB of a pose with a modified reaction coordinate prior to optimization +- **dump_pdb_rc_post_opt**: Dump the PDB of a pose with a modified reaction coordinate after optimization +- **dump_pdb_directory**: Directory in which to dump pre- or post-optimization PDBs, if enabled. Defaults to current directory +- **dry_run**: If true, run through the mover without performing any QM calculations; useful for dumping reaction coordinate PDB files + + +Subtag **ReactionCoordinatePath**: + +- **path_function**: The collection of atomic motions that define the reaction coordinate path;currently, only the 'linear' path function is implemented. +- **path_file**: The file specifying the reaction coordinate atomic start and end states and number of steps. +Lines beginning with '#', '!', '/', '//', or '///' are comment lines. +Uncommented lines are formatted as follows: +PATH_FUNC SET_NUMBER RESIDUE_NUMBER ATOM_NAME START_X START_Y START_Z END_X END_Y END_Z NUMBER_STEPS PATH_FUNC_PARAMS_FILE +PATH_FUNC: defines the functional form of the path connecting the start and end atom coordinates; must be specified in all capital letters; options right now are 'LINEAR'. +SET_NUMBER: tracks which atoms are moved together (i.e., which are in a set together); atoms in the same set must have the same NUMBER_STEPS +RESIDUE_NUMBER: residue number (1-indexed) containing the atom of interest +ATOM_NAME: the atom whose coordinates will be perturbed based on the specified path function and related data +START_X: the starting X coordinate +START_Y: the starting Y coordinate +START_Z: the starting Z coordinate +END_X: the ending X coordinate +END_Y: the ending Y coordinate +END_Z: the ending Z coordinate +NUMBER_STEPS: the number of steps, not the number of states; the discrete xyz coordinates after the initial start xyz coordinates and including the final xyz coordinates; in other words, if you specify 10 steps, then you will end with 11 total discrete states along this path of motion because the reaction coordinate is inclusive of the starting coordinates; for a simple 1D example, consider that for start_coord=0, end_coord=1, NUMBER_STEPS=5 with PATH_FUNC=LINEAR you will have the reaction coordinate of [0, 0.2, 0.4, 0.6, 0.8, 1], which is 6 states separated by 5 steps starting with the initial coordinate PATH_FUNC_PARAMS_FILE: file that specifies additional function parameters for path functions other than 'LINEAR'; not applicable to and ignored for PATH_FUNC=='LINEAR' Here is an example of a valid input line +LINEAR 0 2 H10 23.772 39.889 66.801 23.659 39.187 64.538 10 +The path file may contain as many rows (corresponding to individual atoms) as needed; however, the current implementation will only read the first row (in progress). +- **path_assembly**: Instructions for how to assemble multiple sets of atoms into one reaction coordinate. Complex reaction coordinates may involve multiple atoms moving alone or together either simultaneously, in sequence, combinatorially, or a combination of each. This behavior can be defined through use of SET_NUMBER entries in the 'path_file' and this 'path_assembly' string. Atoms sharing a SET_NUMBER are moved together; however, the behavior of multiple unique set numbers for different atoms is not defined in the 'path_file' - that is addressed with this flag by writing a list of SET_NUMBER values separated by commas and/or enclosed in brackets. Consider the following example: path_assembly='1,2,[3-4],5'. This says that the atoms belonging to SET_NUMBER 1 will be incremented along their reaction coordinate paths first. After that part of the scan is complete, SET_NUMBER 2 will be incremented along the path starting from the end state of SET_NUMBER 1 (note that rules from 'init_rc_from_original_coords' still apply). At the end of SET_NUMBER 2, the space given by combinatorial expansion of all pairwise discrete states of SET_NUMBER 3 and SET_NUMBER 4 will be sampled (so if there are 10 discrete states for SET_NUMBER 3 and 5 discrete states for SET_NUMBER 4 then this step will sample all 50 possible combinations). Finally, SET_NUMBER 5 will be sampled after completion of the previous combinatorial block, beginning from the final state of the previous block. Note also that the path assembly does not need to be written in numeric order (e.g., path_assembly='2,7,5' is valid even if there are additional set numbers in the path file). +- **skip_n_initial_states**: The number of states to skip starting from the initial state after reaction coordinate discretization +- **skip_n_final_states**: The number of states to skip starting from the final state after reaction coordinate discretization + +--- diff --git a/scripting_documentation/RosettaScripts/xsd/mover_ProteinMPNNMover_type.md b/scripting_documentation/RosettaScripts/xsd/mover_ProteinMPNNMover_type.md index 2c78b33e3..cc360751f 100644 --- a/scripting_documentation/RosettaScripts/xsd/mover_ProteinMPNNMover_type.md +++ b/scripting_documentation/RosettaScripts/xsd/mover_ProteinMPNNMover_type.md @@ -4,7 +4,7 @@ _Autogenerated Tag Syntax Documentation:_ --- Author: Frederick Chan (fredchan@uw.edu) -Predict (design) AA identities using the ProteinMPNN deep learning model, and thread the predicted sequence onto the pose. Attempting to use this will result in a runtime error unless Rosetta was successfully compiled with `extras=torch`. +Predict (design) AA identities using the ProteinMPNN deep learning model, and thread the predicted sequence onto the pose. Attempting to use this will result in a runtime error unless Rosetta was successfully compiled with `extras=pytorch`. ```xml + +_Autogenerated Tag Syntax Documentation:_ + +--- +Authors: Benjamin P. Brown (benjamin.p.brown17@gmail.com) +A Residue Selector that selects neighboring residues to a set of residues (focus) based on distance to a collection of user-specified atoms within the focus residues. By default, includes this focus in the resulting selection. + +References and author information for the MultiAtomNeighborhoodSelector residue selector: + +MultiAtomNeighborResidueSelector ResidueSelector's author(s): +Benjamin P. Brown, Department of Chemistry, Vanderbilt University [benjamin.p.brown17@gmail.com] + +```xml + + + +``` + +- **selector**: Focus to select around. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3. +- **resnums**: Focus to select around. +- **distance**: Distance to measure neighbors. Default is 10A. +- **focus_atom_names_for_distance_measure**: A list of comma separated atom names, for each focus residue, the positions of which will be used for measuring distance to find neighbors. +- **search_against_atom_names_for_distance_measure**: A list of comma separated atom names, for each searchable residue, the positions of which will be used for measuring distance to find neighbors. +- **include_focus_in_subset**: Should the focus be included in the returning subset? Default True +- **search_only_by_focus_nbr_atoms**: If true, only search for neighbors based on focus residue NBR atoms (overrides other focus search options). Default False +- **search_by_all_focus_heavy_atoms**: If true, use all heavy atoms in focus residues to identify neighbors. Default True +- **search_by_all_focus_hydrogen_atoms**: If true, use all hydrogen atoms in focus residues to identify neighbors. Default False +- **search_only_against_nbr_atoms**: If true, only search for neighbors against NBR atoms (overrides other focus search options). Default True +- **search_against_all_heavy_atoms**: If true, search against all residue heavy atoms to identify neighbors. Default False +- **search_against_all_hydrogen_atoms**: If true, search against all residue hydrogen atoms to identify neighbors. Default False + + +"Residue Selector Tag": Any of the [[ResidueSelectors]] + +--- diff --git a/scripting_documentation/RosettaScripts/xsd/rs_ResiduePropertySelector_type.md b/scripting_documentation/RosettaScripts/xsd/rs_ResiduePropertySelector_type.md index 3bea96b76..3d790f6a4 100644 --- a/scripting_documentation/RosettaScripts/xsd/rs_ResiduePropertySelector_type.md +++ b/scripting_documentation/RosettaScripts/xsd/rs_ResiduePropertySelector_type.md @@ -12,7 +12,7 @@ A residue selector that selects based on set residue properties. Default is to ``` - **properties**: A comma-separated list of properties for selection. Current choices are: -POLYMER, LIGAND, PROTEIN, CANONICAL_AA, CANONICAL_NUCLEIC, DNA, RNA, TNA, PNA, PEPTOID, OLIGOUREA, ARAMID, ORTHO_ARAMID, META_ARAMID, PARA_ARAMID, PRE_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_META_ARAMID, PRE_METHYLENE_PARA_ARAMID, POST_METHYLENE_ORTHO_ARAMID, POST_METHYLENE_META_ARAMID, POST_METHYLENE_PARA_ARAMID, PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_POST_METHYLENE_META_ARAMID, PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID, CARBOHYDRATE, LIPID, TERPENE, NUCLEOTIDE_DIPHOSPHATE, SRI, TRIAZOLE_LINKER, METAL, SURFACE, WATER, TP3, VIRTUALIZABLE_BY_PACKER, SOLVENT, VIRTUAL_RESIDUE, VRT1, INVERTED_VIRTUAL_RESIDUE, LOWER_TERMINUS, UPPER_TERMINUS, BRANCH_POINT, TERMINUS, LOWERTERM_TRUNC, UPPERTERM_TRUNC, COARSE, ADDUCT, SC_ORBITALS, FRAGMENT, UPPERTERM_CAP, LOWERTERM_CAP, POLAR, HYDROPHOBIC, CHARGED, NEGATIVE_CHARGE, POSITIVE_CHARGE, AROMATIC, ALIPHATIC, CYCLIC, BETA_BRANCHED_SIDECHAIN, METALBINDING, SIDECHAIN_THIOL, DISULFIDE_BONDED, ELECTROPHILE, SIDECHAIN_AMINE, N_METHYLATED, MEMBRANE, PHOSPHONATE, PHOSPHONATE_UPPER, ACETYLATED_NTERMINUS, METHYLATED_CTERMINUS, DIMETHYLATED_CTERMINUS, ALPHA_AA, BETA_AA, GAMMA_AA, L_AA, D_AA, ACHIRAL_BACKBONE, ACHIRAL_SIDECHAIN, R_PEPTOID, S_PEPTOID, TAUTOMER, PURINE, PYRIMIDINE, L_RNA, D_RNA, METHYLATED_NA, TRIOSE, TETROSE, PENTOSE, HEXOSE, HEPTOSE, OCTOSE, NONOSE, ALDOSE, KETOSE, L_SUGAR, D_SUGAR, OXIROSE, OXETOSE, FURANOSE, PYRANOSE, SEPTANOSE, ALPHA_SUGAR, BETA_SUGAR, SIALIC_ACID, C1_MODIFIED, C2_MODIFIED, C3_MODIFIED, C4_MODIFIED, C5_MODIFIED, C6_MODIFIED, C7_MODIFIED, C8_MODIFIED, C9_MODIFIED, GLYCOSIDE, ALDONIC_ACID, URONIC_ACID, DEOXY_SUGAR, AMINO_SUGAR, ACETYLAMINO_SUGAR, GLYCOLYLAMINO_SUGAR, ACETYL_SUGAR, BUTYRYL_SUGAR, LACTYL_SUGAR, R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, PHOSPHORYLATED_SUGAR, SULFATED_SUGAR, SULFOAMINO_SUGAR, THIO_SUGAR, C_METHYLATED_SUGAR, PROPARGYL_SUGAR, FLUORO_SUGAR, METHYL_SUGAR, PHOSPHATE, SPINLABEL, DIAMAGNETIC, PARAMAGNETIC +POLYMER, LIGAND, PROTEIN, CANONICAL_AA, CANONICAL_NUCLEIC, DNA, RNA, TNA, PNA, PEPTOID, OLIGOUREA, ARAMID, ORTHO_ARAMID, META_ARAMID, PARA_ARAMID, PRE_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_META_ARAMID, PRE_METHYLENE_PARA_ARAMID, POST_METHYLENE_ORTHO_ARAMID, POST_METHYLENE_META_ARAMID, POST_METHYLENE_PARA_ARAMID, PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_POST_METHYLENE_META_ARAMID, PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID, CARBOHYDRATE, LIPID, TERPENE, NUCLEOTIDE_DIPHOSPHATE, SRI, TRIAZOLE_LINKER, METAL, SURFACE, WATER, TP3, VIRTUALIZABLE_BY_PACKER, SOLVENT, VIRTUAL_RESIDUE, VRT1, INVERTED_VIRTUAL_RESIDUE, LOWER_TERMINUS, UPPER_TERMINUS, BRANCH_POINT, TERMINUS, LOWERTERM_TRUNC, UPPERTERM_TRUNC, COARSE, ADDUCT, SC_ORBITALS, FRAGMENT, UPPERTERM_CAP, LOWERTERM_CAP, POLAR, HYDROPHOBIC, CHARGED, NEGATIVE_CHARGE, POSITIVE_CHARGE, AROMATIC, ALIPHATIC, CYCLIC, BETA_BRANCHED_SIDECHAIN, METALBINDING, SIDECHAIN_THIOL, DISULFIDE_BONDED, DISULFIDE_SULFHYDRYL, ELECTROPHILE, SIDECHAIN_AMINE, N_METHYLATED, MEMBRANE, PHOSPHONATE, PHOSPHONATE_UPPER, ACETYLATED_NTERMINUS, METHYLATED_CTERMINUS, DIMETHYLATED_CTERMINUS, ALPHA_AA, BETA_AA, GAMMA_AA, L_AA, D_AA, ACHIRAL_BACKBONE, ACHIRAL_SIDECHAIN, R_PEPTOID, S_PEPTOID, TAUTOMER, PURINE, PYRIMIDINE, L_RNA, D_RNA, METHYLATED_NA, TRIOSE, TETROSE, PENTOSE, HEXOSE, HEPTOSE, OCTOSE, NONOSE, ALDOSE, KETOSE, L_SUGAR, D_SUGAR, OXIROSE, OXETOSE, FURANOSE, PYRANOSE, SEPTANOSE, ALPHA_SUGAR, BETA_SUGAR, SIALIC_ACID, C1_MODIFIED, C2_MODIFIED, C3_MODIFIED, C4_MODIFIED, C5_MODIFIED, C6_MODIFIED, C7_MODIFIED, C8_MODIFIED, C9_MODIFIED, GLYCOSIDE, ALDONIC_ACID, URONIC_ACID, DEOXY_SUGAR, AMINO_SUGAR, ACETYLAMINO_SUGAR, GLYCOLYLAMINO_SUGAR, ACETYL_SUGAR, BUTYRYL_SUGAR, LACTYL_SUGAR, R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, PHOSPHORYLATED_SUGAR, SULFATED_SUGAR, SULFOAMINO_SUGAR, THIO_SUGAR, C_METHYLATED_SUGAR, PROPARGYL_SUGAR, FLUORO_SUGAR, METHYL_SUGAR, PHOSPHATE, SPINLABEL, DIAMAGNETIC, PARAMAGNETIC - **logic**: The logic to use for mutliple properties. Default is OR logic. Current choices are: [and_logic, or_logic] diff --git a/scripting_documentation/RosettaScripts/xsd/sfxn_loader_MultiScoreFunction_type.md b/scripting_documentation/RosettaScripts/xsd/sfxn_loader_MultiScoreFunction_type.md new file mode 100644 index 000000000..5dc0afc2b --- /dev/null +++ b/scripting_documentation/RosettaScripts/xsd/sfxn_loader_MultiScoreFunction_type.md @@ -0,0 +1,42 @@ + + +_Autogenerated Tag Syntax Documentation:_ + +--- +Defines a multi scoring function. This is a composite scoring function that applies different scoring functions to different regions of a pose, defined using residue selectors. + +```xml + + + + + + + +``` + +- **dump_pdbs**: FOR DEBUGGING ONLY. If true, a timestamped PDB file is dumped for each region whenever this scoring function is used to score. This is very expensive, and produces a great deal of disk output, when used in a production run! It can also be dangerous when used with MPI or multi-threaded parallel processing, since parallel processes or threads may try to write to disk simultaneously. False by default. + + +Subtag **SimpleCombinationRule**: A MultiScoreFunctionCombinationRule that specifies Russian doll behaviour. The region selected by the first residue selector is scored with the first scoring function. The second scoring function is applied to the union of the regions selected by the first and second residue selectors, and then to the residues selected by the first; the energy of the latter is subtracted from the former. The Nth scoring function is applied to the union fo the regions selected by the first N residue selectors, and then to the union of the first N-1 residue selectors; the energy of the latter is subtracted from the former. The final energy is the sum of all of these differences. + +- **recompute_residue_subsets**: If true, then every time the multiscorefunction containing this combination rule is applied to a Pose, the residue subset of the region is recomputed. If false, then the first computed residue subset is used throughout. For example, if you are performing a proten-ligand interaction energy calculation using the a multiscorefunction, and if your multiscorefunction uses a residue selector built from a distance-based cutoff from the ligand its neighboring residues, then this flag will have potentially undesired behavior. In an interaction energy calculation, the energy is computed twice: once for the complex and again when the protein and ligand are separated in space. When set to true (default), the residue selector separately is applied to the Pose to determine the residues in the region. This means that the residue subsets composing that region will differ between the complexed and the separated energy calculations. In contrast, if this flag is false, then the initial residue subset created from the complex will be recycled for the energy calculation of the separated protein and ligand. Alternatively, if you use an Index residue selector to partition your scoring regions, then this flag will have no impact on the final result because the regions will be determined the same either way. CRITICAL NOTE regarding thread safety - if this flag is false, then the cached data member corresponding to the residue subsets needs to be updated, which means that if multiple threads are using this same object there will be data racing. Please consider your workflow carefully. + +Subtag **Region**: Defines a region of a pose to score with a particular scorefunction in the context of a multiscorefunction. + +- **residue_selector**: The residue selector defining this region to be scored. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3. +- **scorefxn**: The scoring function to use to score this region. + + +Subtag **CappedBondResolutionRule**: A MultiScoreFunctionBondResolutionRule allows chemical capping groups to be added to severed bonds in sub-regions of poses when scored with a MultiScoreFunction. + +- **peptide_nterm_cap**: The type of capping group to add to peptide bonds that are open at the N-terminus. Allowed types are leave_open, hydrogen, acetyl, and methyl. +- **peptide_cterm_cap**: The type of capping group to add to peptide bonds that are open at the C-terminus. Allowed types are leave_open, hydrogen, and methylamide. +- **thiol_cap**: The type of capping group to add to disulfide bond forming groups that have an open bond. Allowed types are leave_open, and sulfhydryl. +- **other_cap**: The type of capping group to add to other open bonds. Allowed types are leave_open. + +--- diff --git a/scripting_documentation/RosettaScripts/xsd/sfxn_loader_ScoreFunction_type.md b/scripting_documentation/RosettaScripts/xsd/sfxn_loader_ScoreFunction_type.md index 1e78e4c86..bea9c51db 100644 --- a/scripting_documentation/RosettaScripts/xsd/sfxn_loader_ScoreFunction_type.md +++ b/scripting_documentation/RosettaScripts/xsd/sfxn_loader_ScoreFunction_type.md @@ -3,7 +3,7 @@ _Autogenerated Tag Syntax Documentation:_ --- -XRW TO DO +Defines a scoring function that can be used in subsequent movers, filters, etc. A scoring function consists of one or more scoring terms, each given a weight. The total score is the sum of each term times its weight. ```xml + ``` - **weights**: A .wts file specifying the relative weights of score terms. - **patch**: A patch file specifying how the relative weights of score terms given in a weights file should be modified. -- **symmetric**: If true, this scorefunction can be used to score symmetric poses. If false, it can only be used on asymmetric poses. -- **hs_hash**: XRW TO DO +- **symmetric**: THIS ATTRIBUTE IS NOW DEPRECATED. It is only included for backwards compatibility. It used to be the case that separate scorefunctions were needed for symmetric or asymmetric poses. In older versions of Rosetta, if true, this scorefunction could be used to score symmetric poses; if false, it could only be used on asymmetric poses. In current Rosetta, any scorefunction can score any pose. +- **hs_hash**: THIS ATTRIBUTE IS DEPRECATED, AND WILL BE REMOVED SOON. Sets the weight of the backbone_stub_constraint scoreterm. This is better done with a 'Reweight' sub-tag. Subtag **Reweight**: @@ -155,6 +206,59 @@ Subtag **Set**: - **buried_unsatisfied_penalty_burial_threshold**: The number of cones in which a point must lie to be considered buried by the method of sidechain neighbor cones, used by the BuriedUnsatPenalty energy. - **buried_unsatisfied_penalty_hbond_energy_threshold**: The energy threshold above which a hydrogen bond is not counted, used by the BuriedUnsatPenalty energy. - **target_clash_pdb**: The target pdb file for clash checking. +- **gamess_path**: Path to GAMESS rungms executable (not including executable name). If not specified, defaults to path set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_path option. +- **gamess_executable_version**: GAMESS executable version. Typically, this is a two-digit string, like 00 or 01. If not specified, this defaults to the executable version specified on the commandline with the -quantum_mechanics:GAMESS:GAMESS_executable_version option. +- **gamess_memory_megabytes**: The amount of memory, in megabytes, that each GAMESS process is allowed to use. Defaults to 8,192 megabytes, or whatever is set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_memory_megabytes commandline flag. +- **gamess_threads**: The number of GAMESS threads to launch. Use 0 to launch one GAMESS thread per hardware thread on the node. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_threads commandline flag. +- **gamess_processes_per_node**: The number of GAMESS MPI processes to launch per node per calling Rosetta thread or process. Use 0 to launch one GAMESS MPI process per hardware thread on the node. Only used if MPI build of GAMESS is used. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_processes_per_node commandline flag. +- **use_gamess_mpi**: If true, the MPI build of GAMESS will be used (which requires a value for gamess processes per node). If not specified, defaults to the commandline setting, based on whether the -quantum_mechanics:GAMESS:GAMESS_processes_per_node option is provided. +- **rosetta_gamess_bridge_temp_directory**: The location of the directory to which we will write temporary files to allow Rosetta to communicate with GAMESS. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:rosetta_GAMESS_bridge_temp_directory commandline flag. +- **clean_rosetta_gamess_bridge_temp_directory**: If true, temporary files written during the Rosetta-GAMESS bridge scratch directory will be deleted. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:clean_rosetta_GAMESS_bridge_temp_directory commandline flag. +- **clean_gamess_scratch_directory**: If true, GAMESS temporary files written during the calculation will be deleted. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:clean_GAMESS_scratch_directory commandline flag. +- **gamess_qm_energy_file_prefix**: The prefix to use for temporary files written by the gamess_qm_energy energy method. Generally, one needn't change this, but it can be useful if one has many instances of Rosetta running on the same system and using the same GAMESS scratch directory or GAMESS supplemental output directory. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_qm_energy_file_prefix commandline flag. +- **gamess_hybrid_molecular_orbital_file**: The path and filename of the GAMESS HMOs.txt file. This is only used for fragment molecular orbital (FMO) calculations. This can be a relative path from the directory that contains the rungms executable or an absolute path. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_hybrid_molecular_orbital_file commandline flag (and rarely needs to be changed). +- **gamess_verbosity**: The overall verbosity level for the GAMESS output log. Allowed options are 'maximal', 'normal', and 'minimal', and these correspond to NPRINT=9, NPRINT=7, and NPRINT=-5, respectively, in the $CONTRL block of the GAMESS input file. Note that fragment molecular orbital (FMO) verbosity is set separately with the default_fmo_verbosity flag. If not specified, this defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:default_verbosity commandline flag. +- **gamess_solvent**: The solvent to use. Common choics are GAS (no solvent) and WATER. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_solvent flag. +- **gamess_use_smd_solvent**: If true, use the Solvation Model Density (SMD) with CDS corrections; otherwise, use a standard polarizable continuum model for solvation. +- **gamess_basis_set**: The basis set to use for point energy calculation. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_basis_set flag. +- **gamess_ngaussian**: The number of Gaussians to include in the basis set. Only used for some basis sets. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_ngaussian flag. +- **gamess_npfunc**: The number of light-atom (H, He) P-orbital basis functions to include in the basis set. Not used by all basis functions; see the GAMESS documentation for details. Maximum 3. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_npfunc flag. +- **gamess_ndfunc**: The number of heavyatom D-orbital basis functions to include in the basis set. Not used by all basis functions; see the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_ndfunc flag. +- **gamess_nffunc**: The number of heavyatom F-orbital basis functions to include in the basis set. Not used by all basis functions; see the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_nffunc flag. +- **gamess_diffsp**: Should a diffuse SP shell be added to heavyatoms? See the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_diffsp flag. +- **gamess_diffs**: Should a diffuse S shell be added to hydrogen atoms? See the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_diffs flag. +- **gamess_dft_functional**: The DFT functional to use, if density functional theory is specified. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_dft_functional flag. +- **gamess_dft_dispersion_corrections**: The DFT dispersion correction to use, specified as an integer. Use -1 to use GAMESS default, 0 for None, 1 for Grimme's DC 2004, 2 for Grimme's DC 2006 (DFT-D2, the default in wB97X-D and B97-D), 3 for Grimme's DC 2010 (DFT-D3, GAMESS default if DC is requested), or 4 for modified DFT-D3 (DFT-D3(BJ), the default for HF-3C). If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_dft_dispersion_corrections flag. +- **gamess_multiplicity**: The multiplicity. Typically 1, unless free radicals are present. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_multiplicity flag. +- **gamess_electron_correlation_treatment**: The electron correlation treatment. Options are HF, SE (semi-empirical), MP2 (Moller-Plesset perturbation theory 2nd order corrections), or DFT (density functional theory). If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_electron_correlation_treatment flag. +- **gamess_max_scf_iterations**: The number of self-consistent field iteration cycles. A setting of 0 (the default) uses the GAMESS default (which is 30 in most circumstances). It is recommended to set this higher for larger peptides or for any protein. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_max_scf_iterations flag. +- **gamess_use_scf_damping**: If true, Davidson damping is applied to aid SCF convergence when doing GAMESS calculations. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:default_use_scf_damping flag. +- **gamess_fmo_calculation**: If true, we perform a fragment molecular orbital calculation based on the rules set in the scorefunction for dividing a pose into fragments. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_fmo_calculation flag. +- **gamess_max_fmo_monomer_scf_iterations**: The maximum number of monomer SCF iterations to perform by default. If not provided, defaults to whatever is provided on the commandline with the -quantum_mechanics:GAMESS:default_max_fmo_monomer_scf_iterations flag. +- **gamess_hybrid_molecular_orbital**: The precomputed hybrid molecular orbital, listed in the GAMESS HMOs.txt file, that should be used at cutpoint atoms when doing a fragment molecular orbital calculation with GAMESS. Only used for FMO calculations. If not specified, defaults to whatever is specified on the commandline with the -quantum_mechanics:GAMESS:gamess_hybrid_molecular_orbital flag. +- **gamess_symmetry**: The symmetry expected by the gamess_qm_energy energy term. NONE can always be used, though for symmetric molecules, this makes the QM calculation less efficient than it could be. Allowed types are: NONE, Cn, Dn, and Sn. The symmetry of the pose must match the symmetry specfied! If not specified, this defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_qm_energy_symmetry flag. +- **gamess_symmetry_n**: The n-fold symmetry expected by the gamess_qm_energy energy term. This must be an integer greater than 1 if symmetry is Cn or Dn, and an even integer greater than 1 if symmetry is Sn. Not used if symmetry is NONE. +- **gamess_fmo_verbosity**: The amount of output in the logfile from an FMO calculation. The options 'normal', 'reduced', 'small', and 'minimal' correspond to NPRINT=0, 1, 2, and 3 respectively in the $FMOPRP group in the GAMESS input file. If not specified, defaults to whatever is specified on the commandline with the -quantum_mechanics:GAMESS:fmo_verbosity option. +- **gamess_qm_energy_geo_opt**: Should the gamess_qm_energy scoreterm geometry-optimize the input pose before returning a final score? Note that if this option is used, the optimized geometry is NOT returned; only the score. This is also much slower. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_qm_energy_geo_opt flag. +- **gamess_error_on_nonideal_bond_length_after_opt**: If true, Rosetta will throw an error if a GAMESS geometry optimization breaks a covalent bond (results in nonideal bond lengths over or under a threshold). If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_error_on_nonideal_bond_length_after_opt flag. +- **gamess_nonideal_bond_length_fract_threshold**: The fractional threshold for detecting nonideal bond lenghts. For example, if set to 0.35, Rosetta throws an error if any bond is detected that is 35% longer or shorter than ideal after GAMESS geometry optimization. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_nonideal_bond_length_fract_threshold flag. +- **gamess_geo_opt_max_steps**: The maximum number of geometry optimization steps that will be carried out, if GAMESS is optimizing geometry. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_max_steps flag. +- **gamess_geo_opt_tolerance**: The tolerance for geometry optimization, if GAMESS is optimizing geometry. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_max_steps flag. +- **gamess_immobilize_h_bond_lengths**: If true, use GAMESS IFZMAT to freeze covalent bond lengths to hydrogen atoms to equilibrium values. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_immobilize_h_bond_lengths. +- **gamess_use_h_bond_length_constraints**: If true, use GAMESS IHMCON to harmonically constrain covalent bond lengths to hydrogen atoms to equilibrium values. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_constrain_h_bond_lengths. +- **gamess_h_bond_length_constraint_force**: If 'gamess_constrain_h_bond_lengths' is true and this flag is set, set the GAMESS FHMCON constraint force (kcal/mol) to this value. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_h_bond_length_constraint_force. +- **gamess_freeze_atoms_cart**: List of atom indices to be frozen during geometry optimization; set the GAMESS IFREEZ option to freeze an atom in Cartesian space; incompatible with NZVAR greater than 0 because the constraint is in Cartesian space; default behavior is to not freeze any atoms +- **gamess_freeze_atoms_by_res_cart**: Atoms given in the format 'ResNum.AtomName' to be frozen during geometry optimization; set the GAMESS IFREEZ option to freeze an atom in Cartesian space; incompatible with NZVAR greater than 0 because the constraint is in Cartesian space; default behavior is to not freeze any atoms +- **gamess_dftb_taylor_expansion_order**: The density functional tight binding (DFTB) semi-empirical method is fast since it uses only the first few terms of a Taylor series expansion of the Kohn/Sham DFT total energy. This parameter (equivalent to NDFTB in a GAMESS input file) determines how many terms to use. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_taylor_expansion_order; can be set to 1, 2, or 3. +- **gamess_use_dftb_long_range_correction**: This turns on the long range corretion to the DFTB semi-empirical method. Note that this requires parameters optimized for the long-range correction. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_use_dftb_long_range_correction. This is equivalent to the LCDFTB option in a GAMESS input file. +- **gamess_dftb_long_range_correction_parameter**: A configuration parameter for the DFTB long-range correction. Only used if gamess_use_dftb_long_range_correction is set to true. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_long_range_correction_parameter. See the EMU option in the GAMESS documentation for details. +- **gamess_use_dftb_damping_function_for_X_H**: If true, a damping function for X-H atomic pair interactions is included in the DFTB semi-empirical method. Requires gamess_dftb_taylor_expansion_order to be set to 3. See the DAMPXH option in the GAMESS documentation for details. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_use_dftb_damping_function_for_X_H. +- **gamess_dftb_damping_exponent_for_X_H**: The exponent for the damping function added for X-H atomic pairs. Only used if gamess_use_dftb_damping_function_for_X_H is set to true. If not provided, whatever is provided on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_damping_exponent_for_X_H is used. See the DAMPEX option in the GAMESS documentation for details. +- **gamess_use_dftb_shell_resolved_scc**: If true, shell-resolved SCC calculations are performed. Requires gamess_dftb_taylor_expansion_order to be set to 1 or 2. Defaults to whatever is provided on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_use_dftb_shell_resolved_scc. See the SRSCC option in the GAMESS documentation for details. +- **gamess_dftb_convergence_method**: The convergence method used for SCC calculations. Defaults to whatever is set on the commandline with the -quantum_mehanics:GAMESS:dftb:gamess_dftb_convergence_method option. Allowed values are standard, Broyden, DIIS. See the ITYPMX option in the GAMESS documentation for details. +- **gamess_dftb_electronic_temperature**: Electronic temperature in Kelvin to help convergence of nearly-degenerate systems. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_electronic_temperature. See the ETEMP option in the GAMESS documentation for details. +- **gamess_dftb_dispersion_model**: The dispersion correction model for DFTB calculations. Allowed values are NONE, UFF, SK, SKHP, and DFT. Defaults to whatever is set on the commandline with the -quantum_mehanics:GAMESS:dftb:gamess_dftb_dispersion_model option. See the DISP option in the GAMESS documentation for details. +- **gamess_dftb_parameters_directory**: The directory (relative to the GAMESS_path/auxdata/DFTB/ directory) in which DFTB parameters are found. If not set, the commandline option -quantum_mehanics:GAMESS:dftb:gamess_dftb_parameters_directory is used. If nothing is set here or on the commandline, this defaults to 3OB-3-1, which is suitable for Taylor expanson level 3 and aqueous solvent. See the PARAM option in the GAMESS documentation for details. - **dump_trajectory_prefix**: If the dump_trajectory scoreterm is used, this is the prefix for the filename to which we're dumping. - **dump_trajectory_gz**: If the dump_trajectory scoreterm is used, this determines whether we write to gzipped files. False by defualt. - **dump_trajectory_stride**: If the dump_trajectory scoreterm is used, this is the frequency with which we write. Every Nth evaluation of the score term, a pose will be written. Default 1. @@ -167,4 +271,8 @@ Subtag **Set**: - **hbnet_bonus_function_ramping**: The hbnet score term's bonus function can scale in different ways as the size of a network grows. The default is quadratic growth, though linear, logarithmic, and square root growth are all allowed. - **hbnet_max_network_size**: The maximum size of a hydrogen bond network, beyond which the hbnet score term no longer gives a bonus. Defaults to 0 (unlimited). +Subtag **QMConfiguration**: Defines options for quantum mechanics scoreterms in this scorefunction. + +- **fmo_fragmentation_method**: The fragmentation method to use to divide a large pose into small fragments for fragment molecular orbital methods. Defaults to carbon_carbon_favouring_residue_based_fragments. Allowed options are: residue_based_fragments, and carbon_carbon_favouring_residue_based_fragments. + --- diff --git a/scripting_documentation/RosettaScripts/xsd/simple_metric_GamessQMEnergyMetric_type.md b/scripting_documentation/RosettaScripts/xsd/simple_metric_GamessQMEnergyMetric_type.md new file mode 100644 index 000000000..1d13001f7 --- /dev/null +++ b/scripting_documentation/RosettaScripts/xsd/simple_metric_GamessQMEnergyMetric_type.md @@ -0,0 +1,122 @@ + + +_Autogenerated Tag Syntax Documentation:_ + +--- +A simple metric that caches in the pose a QM energy externally computed with GAMESS, plus additional values from the calculation. + +```xml + + + +``` + +- **custom_type**: Allows multiple configured SimpleMetrics of a single type to be called in a single RunSimpleMetrics and SimpleMetricFeatures. + The custom_type name will be added to the data tag in the scorefile or features database. +- **use_cached_QM_energy**: If true, we first check the pose for a previous QM energy calculation that isn't stale (i.e. the pose hasn't changed) and which used the same level of theory. The result of that is retrieved if possible, and a new QM calculation performed only if we don't already have a QM result. If false, we always redo the QM energy calculation. True by default to avoid unnecessarily repeated computations. +- **gamess_path**: Path to GAMESS rungms executable (not including executable name). If not specified, defaults to path set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_path option. +- **gamess_executable_version**: GAMESS executable version. Typically, this is a two-digit string, like 00 or 01. If not specified, this defaults to the executable version specified on the commandline with the -quantum_mechanics:GAMESS:GAMESS_executable_version option. +- **gamess_memory_megabytes**: The amount of memory, in megabytes, that each GAMESS process is allowed to use. Defaults to 8,192 megabytes, or whatever is set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_memory_megabytes commandline flag. +- **gamess_threads**: The number of GAMESS threads to launch. Use 0 to launch one GAMESS thread per hardware thread on the node. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_threads commandline flag. +- **gamess_processes_per_node**: The number of GAMESS MPI processes to launch per node per calling Rosetta thread or process. Use 0 to launch one GAMESS MPI process per hardware thread on the node. Only used if MPI build of GAMESS is used. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:GAMESS_processes_per_node commandline flag. +- **use_gamess_mpi**: If true, the MPI build of GAMESS will be used (which requires a value for gamess processes per node). If not specified, defaults to the commandline setting, based on whether the -quantum_mechanics:GAMESS:GAMESS_processes_per_node option is provided. +- **rosetta_gamess_bridge_temp_directory**: The location of the directory to which we will write temporary files to allow Rosetta to communicate with GAMESS. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:rosetta_GAMESS_bridge_temp_directory commandline flag. +- **clean_rosetta_gamess_bridge_temp_directory**: If true, temporary files written during the Rosetta-GAMESS bridge scratch directory will be deleted. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:clean_rosetta_GAMESS_bridge_temp_directory commandline flag. +- **clean_gamess_scratch_directory**: If true, GAMESS temporary files written during the calculation will be deleted. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:clean_GAMESS_scratch_directory commandline flag. +- **gamess_qm_energy_file_prefix**: The prefix to use for temporary files written by the gamess_qm_energy energy method. Generally, one needn't change this, but it can be useful if one has many instances of Rosetta running on the same system and using the same GAMESS scratch directory or GAMESS supplemental output directory. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_qm_energy_file_prefix commandline flag. +- **gamess_hybrid_molecular_orbital_file**: The path and filename of the GAMESS HMOs.txt file. This is only used for fragment molecular orbital (FMO) calculations. This can be a relative path from the directory that contains the rungms executable or an absolute path. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_hybrid_molecular_orbital_file commandline flag (and rarely needs to be changed). +- **gamess_verbosity**: The overall verbosity level for the GAMESS output log. Allowed options are 'maximal', 'normal', and 'minimal', and these correspond to NPRINT=9, NPRINT=7, and NPRINT=-5, respectively, in the $CONTRL block of the GAMESS input file. Note that fragment molecular orbital (FMO) verbosity is set separately with the default_fmo_verbosity flag. If not specified, this defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:default_verbosity commandline flag. +- **solvent**: The solvent to use. Common choics are GAS (no solvent) and WATER. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_solvent flag. +- **use_smd_solvent**: If true, use the Solvation Model Density (SMD) with CDS corrections; otherwise, use a standard polarizable continuum model for solvation. +- **basis_set**: The basis set to use for point energy calculation. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_basis_set flag. +- **ngaussian**: The number of Gaussians to include in the basis set. Only used for some basis sets. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_ngaussian flag. +- **npfunc**: The number of light-atom (H, He) P-orbital basis functions to include in the basis set. Not used by all basis functions; see the GAMESS documentation for details. Maximum 3. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_npfunc flag. +- **ndfunc**: The number of heavyatom D-orbital basis functions to include in the basis set. Not used by all basis functions; see the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_ndfunc flag. +- **nffunc**: The number of heavyatom F-orbital basis functions to include in the basis set. Not used by all basis functions; see the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_nffunc flag. +- **diffsp**: Should a diffuse SP shell be added to heavyatoms? See the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_diffsp flag. +- **diffs**: Should a diffuse S shell be added to hydrogen atoms? See the GAMESS documentation for details. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_diffs flag. +- **dft_functional**: The DFT functional to use, if density functional theory is specified. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_dft_functional flag. +- **dft_dispersion_corrections**: The DFT dispersion correction to use, specified as an integer. Use -1 to use GAMESS default, 0 for None, 1 for Grimme's DC 2004, 2 for Grimme's DC 2006 (DFT-D2, the default in wB97X-D and B97-D), 3 for Grimme's DC 2010 (DFT-D3, GAMESS default if DC is requested), or 4 for modified DFT-D3 (DFT-D3(BJ), the default for HF-3C). If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_dft_dispersion_corrections flag. +- **multiplicity**: The multiplicity. Typically 1, unless free radicals are present. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_multiplicity flag. +- **electron_correlation_treatment**: The electron correlation treatment. Options are HF, SE (semi-empirical), MP2 (Moller-Plesset perturbation theory 2nd order corrections), or DFT (density functional theory). If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_electron_correlation_treatment flag. +- **max_scf_iterations**: The number of self-consistent field iteration cycles. A setting of 0 (the default) uses the GAMESS default (which is 30 in most circumstances). It is recommended to set this higher for larger peptides or for any protein. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:default_max_scf_iterations flag. +- **use_scf_damping**: If true, Davidson damping is applied to aid SCF convergence when doing GAMESS calculations. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:default_use_scf_damping flag. +- **fmo_calculation**: If true, we perform a fragment molecular orbital calculation based on the rules set in the scorefunction for dividing a pose into fragments. If not specified, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_fmo_calculation flag. +- **max_fmo_monomer_scf_iterations**: The maximum number of monomer SCF iterations to perform by default. If not provided, defaults to whatever is provided on the commandline with the -quantum_mechanics:GAMESS:default_max_fmo_monomer_scf_iterations flag. +- **hybrid_molecular_orbital**: The precomputed hybrid molecular orbital, listed in the GAMESS HMOs.txt file, that should be used at cutpoint atoms when doing a fragment molecular orbital calculation with GAMESS. Only used for FMO calculations. If not specified, defaults to whatever is specified on the commandline with the -quantum_mechanics:GAMESS:gamess_hybrid_molecular_orbital flag. +- **symmetry**: The symmetry expected by the gamess_qm_energy energy term. NONE can always be used, though for symmetric molecules, this makes the QM calculation less efficient than it could be. Allowed types are: NONE, Cn, Dn, and Sn. The symmetry of the pose must match the symmetry specfied! If not specified, this defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_qm_energy_symmetry flag. +- **symmetry_n**: The n-fold symmetry expected by the gamess_qm_energy energy term. This must be an integer greater than 1 if symmetry is Cn or Dn, and an even integer greater than 1 if symmetry is Sn. Not used if symmetry is NONE. +- **fmo_verbosity**: The amount of output in the logfile from an FMO calculation. The options 'normal', 'reduced', 'small', and 'minimal' correspond to NPRINT=0, 1, 2, and 3 respectively in the $FMOPRP group in the GAMESS input file. If not specified, defaults to whatever is specified on the commandline with the -quantum_mechanics:GAMESS:fmo_verbosity option. +- **gamess_qm_energy_geo_opt**: Should the gamess_qm_energy scoreterm geometry-optimize the input pose before returning a final score? Note that if this option is used, the optimized geometry is NOT returned; only the score. This is also much slower. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_qm_energy_geo_opt flag. +- **error_on_nonideal_bond_length_after_opt**: If true, Rosetta will throw an error if a GAMESS geometry optimization breaks a covalent bond (results in nonideal bond lengths over or under a threshold). If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_error_on_nonideal_bond_length_after_opt flag. +- **nonideal_bond_length_fract_threshold**: The fractional threshold for detecting nonideal bond lenghts. For example, if set to 0.35, Rosetta throws an error if any bond is detected that is 35% longer or shorter than ideal after GAMESS geometry optimization. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_nonideal_bond_length_fract_threshold flag. +- **geo_opt_max_steps**: The maximum number of geometry optimization steps that will be carried out, if GAMESS is optimizing geometry. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_max_steps flag. +- **geo_opt_tolerance**: The tolerance for geometry optimization, if GAMESS is optimizing geometry. If not specied, defaults to what is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_max_steps flag. +- **immobilize_h_bond_lengths**: If true, use GAMESS IFZMAT to freeze covalent bond lengths to hydrogen atoms to equilibrium values. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_immobilize_h_bond_lengths. +- **use_h_bond_length_constraints**: If true, use GAMESS IHMCON to harmonically constrain covalent bond lengths to hydrogen atoms to equilibrium values. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_constrain_h_bond_lengths. +- **h_bond_length_constraint_force**: If 'gamess_constrain_h_bond_lengths' is true and this flag is set, set the GAMESS FHMCON constraint force (kcal/mol) to this value. If not specified, defaults to whatever is set on the commandline with the -quantum_mechanics:GAMESS:gamess_geo_opt_h_bond_length_constraint_force. +- **freeze_atoms_cart**: List of atom indices to be frozen during geometry optimization; set the GAMESS IFREEZ option to freeze an atom in Cartesian space; incompatible with NZVAR greater than 0 because the constraint is in Cartesian space; default behavior is to not freeze any atoms +- **freeze_atoms_by_res_cart**: Atoms given in the format 'ResNum.AtomName' to be frozen during geometry optimization; set the GAMESS IFREEZ option to freeze an atom in Cartesian space; incompatible with NZVAR greater than 0 because the constraint is in Cartesian space; default behavior is to not freeze any atoms +- **dftb_taylor_expansion_order**: The density functional tight binding (DFTB) semi-empirical method is fast since it uses only the first few terms of a Taylor series expansion of the Kohn/Sham DFT total energy. This parameter (equivalent to NDFTB in a GAMESS input file) determines how many terms to use. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_taylor_expansion_order; can be set to 1, 2, or 3. +- **use_dftb_long_range_correction**: This turns on the long range corretion to the DFTB semi-empirical method. Note that this requires parameters optimized for the long-range correction. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_use_dftb_long_range_correction. This is equivalent to the LCDFTB option in a GAMESS input file. +- **dftb_long_range_correction_parameter**: A configuration parameter for the DFTB long-range correction. Only used if use_dftb_long_range_correction is set to true. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_long_range_correction_parameter. See the EMU option in the GAMESS documentation for details. +- **use_dftb_damping_function_for_X_H**: If true, a damping function for X-H atomic pair interactions is included in the DFTB semi-empirical method. Requires dftb_taylor_expansion_order to be set to 3. See the DAMPXH option in the GAMESS documentation for details. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_use_dftb_damping_function_for_X_H. +- **dftb_damping_exponent_for_X_H**: The exponent for the damping function added for X-H atomic pairs. Only used if use_dftb_damping_function_for_X_H is set to true. If not provided, whatever is provided on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_damping_exponent_for_X_H is used. See the DAMPEX option in the GAMESS documentation for details. +- **use_dftb_shell_resolved_scc**: If true, shell-resolved SCC calculations are performed. Requires dftb_taylor_expansion_order to be set to 1 or 2. Defaults to whatever is provided on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_use_dftb_shell_resolved_scc. See the SRSCC option in the GAMESS documentation for details. +- **dftb_convergence_method**: The convergence method used for SCC calculations. Defaults to whatever is set on the commandline with the -quantum_mehanics:GAMESS:dftb:gamess_dftb_convergence_method option. Allowed values are standard, Broyden, DIIS. See the ITYPMX option in the GAMESS documentation for details. +- **dftb_electronic_temperature**: Electronic temperature in Kelvin to help convergence of nearly-degenerate systems. Defaults to whatever is set on the commandline with -quantum_mehanics:GAMESS:dftb:gamess_dftb_electronic_temperature. See the ETEMP option in the GAMESS documentation for details. +- **dftb_dispersion_model**: The dispersion correction model for DFTB calculations. Allowed values are NONE, UFF, SK, SKHP, and DFT. Defaults to whatever is set on the commandline with the -quantum_mehanics:GAMESS:dftb:gamess_dftb_dispersion_model option. See the DISP option in the GAMESS documentation for details. +- **dftb_parameters_directory**: The directory (relative to the GAMESS_path/auxdata/DFTB/ directory) in which DFTB parameters are found. If not set, the commandline option -quantum_mehanics:GAMESS:dftb:gamess_dftb_parameters_directory is used. If nothing is set here or on the commandline, this defaults to 3OB-3-1, which is suitable for Taylor expanson level 3 and aqueous solvent. See the PARAM option in the GAMESS documentation for details. + + +Subtag **QMConfiguration**: Defines options for quantum mechanics scoreterms in the scorefunction used when scoring with this metric. + +- **fmo_fragmentation_method**: The fragmentation method to use to divide a large pose into small fragments for fragment molecular orbital methods. Defaults to carbon_carbon_favouring_residue_based_fragments. Allowed options are: residue_based_fragments, and carbon_carbon_favouring_residue_based_fragments. + +---